I don't think this is a problem with NOD, your just not used to playing a different faction yet. From the word go, I wanted to hit NOD and use them, but by the time I unlocked them, I found them to not be nearly as strong as my GDI. So instead, I kept maining my GDI until I could build a good NOD deck.
To counter the flame tank, literally use anything but infantry. A predator at 60 tib will murder a 140 tib flame tank. That's half the price, and it wins.
The Rockworm is a vehicle destroyer. Use infantry, or even better, air. An orca will bomb a rockworm mercilessly. And it is cheaper. Look at the units, learn their counters, and build a balanced deck.
Lastly, stop going double harvester. If the enemy goes double, send over units to kill theirs. Not only will that net you free money, but you put them at an eco disadvantage. If you let them mass flame tanks and rockworms, there is only one person to blame, and it's not your opponent.